Delenn explains to Lennier that she has been asked to appear before the Grey Council. A new leader has been chosen for the Council and they wish to discuss her current role: both as a member of the Council and as ambassador to Babylon 5. She admits to Lennier that she is afraid she might not be coming back, as her transformation has obviously caused division.

In C'n'C, Commander Ivanova briefs Captain Sheridan regarding some recent ships going missing within their sector. Neither believes it is the work of raiders and agree someone should investigate. Sheridan decides that he will take a Starfury wing out. Ivanova is not happy with the decision, but Sheridan insists it is hardly a clear and present danger he's flying into.

In deep space, a NarnFrazi class heavy fighter is attacked by an unknown alien vessel. The pilot ejects as his ship is destroyed and his pod is picked up by the attacking ship.

Lennier informs Delenn that her Minbari flyer is ready for her. He also tells her that he has borrowed a flyer for his own use, wishing to accompany her on her journey. Delenn objects, as she does not want any disfavor the Council has for her to imprint onto him. Lennier is not concerned, however, and insists on going along. Delenn relents and says she appreciates the company.

As Sheridan prepares for his mission, Ivanova links him with a message that General William Hague will be arriving ahead of schedule. Ivanova is stunned that the Captain did not inform her that a member of the Joint Chiefs of Staff was coming, but Sheridan insists it is merely an informal, cordial visit. He also assures her that he will be back from his patrol well before he arrives.

Later, Delenn and Lennier arrive at the Grey Council's ship. Lennier waits in the hallway while Delenn proceeds to the Grey Council Chamber.

In another part of space, Sheridan's wing arrive through the local jumpgate and scan for any signs of the missing ships. It's quiet until they start to head back. A strange alien ship suddenly jumps into local space and attacks them. Sheridan's ship is badly damaged and he has to eject. All ships in his wing are destroyed save for Ramirez, though his fighter is badly damaged. The alien ship picks up Sheridan's cockpit and jumps back into hyperspace.

Ramirez struggles to get his damaged fighter back online. The ship reports a radiation leak in the reactor and that the communication systems are offline. Knowing the only hope the captain has for rescue is for him to get back, he enters the jumpgate and heads back to the station (despite the radiation level already being at terminal levels).

General Hague arrives on Babylon 5 and is greeted by Commander Ivanova. He notes that Sheridan is not present, insisting that Sheridan would never keep him waiting, but Ivanova doesn't seem to be worried.

Sheridan awakens aboard the alien vessel, strapped to a table. A series of automated instruments descends from the ceiling, moving towards him.

Delenn appears in a conspicuously empty Grey Council Chamber. Hedronn appears alone. He informs her that the Council will not appear, as she has been summoned to receive judgment. Her fate has apparently already been decided, and for her act of defiance (undergoing her transformation) she has been stripped of her position in the Council. Delenn asks about her role as Ambassador, and Hedronn says the Council is still debating. He offers to allow her to speak before the Council on the matter and she eagerly accepts.

Ramirez fortunately makes it back to Babylon 5. Ivanova detects the critical condition of the fighter and the pilot from C'n'C.

After being experimented upon, Sheridan calls out, but the only answer is a metal rod dropped to his side. He is then released from his bindings and attacked by a Drazi wielding a similar weapon. The Drazi has a device on his head that seems to be compelling his attack. Sheridan defends himself, pleading to the Drazi to fight the control. Suddenly, the Drazi is killed by a third prisoner: a Narn wielding a sword who also has one of the control devices on him.

The Narn prisoner then attacks Sheridan. The Captain is just barely able to defend himself. Oddly, as they fight, the Narn begs Sheridan to kill him. Sheridan refuses, but does knock him out.

Dr. Franklin frantically tries to treat Ramirez, but the pilot dies from the radiation poisoning. Ivanova discusses the captain's kidnapping with Garibaldi, though as being completely alien they do not know where to start looking for it.

Delenn pleads her case before the Grey Council, asking them to allow her to continue her mission at Babylon 5. Her replacement then reveals himself, and she is both shocked and angered to see that it is Neroon, a member of the Warrior Caste. This means the Council now has 4 members from the Warrior Caste and only 2 from the Religious Caste, tipping the balance. Neroon angrily confronts Delenn, calling her transformation obscene and insisting that the Warrior Caste has the right to lead given all their sacrifices. He also declares that if the prophecies Delenn believes in are indeed about to come true – that a great war is coming – then the Warrior Caste has all the more right to lead. He states that she should remain on Babylon 5, as she no longer belongs among the Minbari.

The Narn prisoner awakens, still injured from the fight. Sheridan has disabled the device that was controlling him. The Narn believes they were picked up as part of a scouting mission for potential invasion. Sheridan asks the Narn why he asked him to kill him, and the Narn replies that there is no escape – better to die. He then passes out again.

Delenn emerges from the Council Chamber and approaches Lennier. She explains what happened (though leaves out how ugly it got). She offers him a chance to leave her service, but he does not need a moment to consider the offer. He will stand by her side, no matter what the future brings, and she is grateful for it.

General Hague discusses the alien ship with Ivanova. She confirms that the ship has been sighted a few more times, but they still have not been able to identify it. The EAS Agamemnon arrives, Hague having called it there to help in the search.

Sheridan falls asleep aboard the alien ship and has a strange dream filled with cryptic messages: Ivanova asking "Do you know who I am?" and telling him "You are the hand"; Garibaldi telling him "The Man in between is searching for you"; and even the image of Sheridan himself wearing a Psi Cop uniform. Finally, he sees Kosh, who tells him that "this is the first time your mind has been quiet enough to hear me." Sheridan asks, "Why am I here?" and Kosh replies, "You have always been here." Sheridan awakens to the sound of part of the wall nearby shifting upward a couple of inches. He decides to use the metal weapon he was given as a lever.

Delenn and Lennier head back to Babylon 5. On the way, Delenn is alerted to the captain's kidnapping. After they send her the information, she contacts Ivanova with some valuable information: the alien race is known as the Streib, and they once tried playing their game with the Minbari, who taught them the depth of their mistake. She sends the coordinates of the Streib homeworld to the station.

Sheridan continues trying to pry open the door. The Narn awakens and begins to help him. The ship shudders suddenly, and Sheridan guesses they have just jumped into normal space. The ship shudders again a moment later, this time more violently – clearly the ship is under attack.

The Agamemnon and a Babylon 5 fighter squadron (led by Ivanova) attack the Streib vessel in orbit over their homeworld. Delenn has come along in her flyer. She sends a signal to the Streib, demanding they release their prisoners.

Sheridan and the Narn escape their cell. Together they find an escape pod and enter it.

Ivanova watches helplessly as the Streib ships launches its prisoners into space. Horrified, she orders the Agamemnon to take the ship down. The Agamemnon complies and the Streib ship is completely destroyed. Fortunately, Ivanova detects a life pod, but realizes the signal emanating from it is morse code and concludes it has Sheridan aboard.

Back on the station, Sheridan and the Narn are treated in Medlab. Franklin gives Sheridan the bad news about Ramirez. After the captain leaves Medlab, he sees Kosh, who tells him simply "You have always been here."

Later, Sheridan is met by General Hague in his quarters. After a couple pleasantries, Hague activates a jamming device in case the room is bugged. Sheridan has been expecting this and explains how frustrated he is, having been on his assignment six months without anyone coming out to debrief him. Sheridan reports that the officers are all loyal to Earth and he is not happy about having had to spy on them all year. Hague explains that it was necessary, given the rumors regarding the death of PresidentSantiago, since if it was a coup then the conspirators would have had to have help from within the military. Both men speculate that Psi Corps might have been involved. Hague believes Sheridan can operate free from close scrutiny by President Clark, being a valuable asset to Hague's cause. He is determined to start uncovering the truth about what is happening at home, and asks Sheridan to stand with him.

After Hague departs the station, Sheridan has Ivanova, Garibaldi, and Franklin over for a late night discussion. He asks them to help him and his allies to start quietly investigating what is happening to their government and their home. All three of them agree to stand him, wherever it leads.

It is revealed that Sheridan has been secretly working with General Hague ever since he first came aboard to investigate suspicious activities within EarthGov. He reveals this to his senior staff and they are drawn into it with him.

It also foreshadows Sheridan's meeting with Justin, the middle-man or "man-in-between", in "Z'ha'dum".

It also shows Kosh's vested interest in Sheridan for the first time as he not only sent the dream but also hints at this fact when he tells the Captain the very same thing he told him in the dream when he is back on Babylon 5: "You have always been here."